Acta Cryst. (2006). D62, 678-682 [ doi:10.1107/S0907444906014594 ]
Abstract: A new analysis has been made of distances around metal sites in protein structures in the Protein Data Bank determined with resolution ![[less-than or equal to]](/logos/entities/le_rmgif.gif)
1.25 Å and equivalent distances have been extracted from the Cambridge Structural Database. They are for the metals Na, Mg, K, Ca, Mn, Fe, Co, Cu, Zn and the donor atoms O of water, O of Asp and Glu, O of the main-chain carbonyl group, N of His and S of Cys. Some revisions are recommended to the tables of `target distances' previously given [Harding (2001), Acta Cryst. D57, 401-411; Harding (2002), Acta Cryst. D58, 872-874]. As well as small changes in many distances and a large improvement for Mg-Ocarboxylate, the table includes an indication of how reliable each prediction may be. Special attention was given to carboxylate interactions. When the carboxylate group is monodentate, the M-Ocarboxylate distance is well defined, but for bidentate carboxylate groups a wide range of distances is allowable; when the metal is Co, Cu or Zn the M-O1 and M-O2 distances are clearly inversely correlated; for the more purely electrostatic interactions involving Na, K and Ca there is a wider scatter of distances and little correlation.
Keywords: metal sites; distances; target distances; carboxylates; atomic resolution.
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